Re plug color, Generally darker colors will better hilite reflection from indirect light & contrast more so you will be able to see any underlying waviness (the polished potatoe syndrome) as well as gloss. Dont make it black if you are for example using black tooling gel on the female mold. A different underlying plug color can help show if tooling gel might be thin like on sharper corners or the apex of a plug. Generally dark female molds are better for hand layups, but if you are pre-painting or vac bagging, its not that big a deal.

Im not a paint expert but I think clears are formulated for buffing & polishing whereas pigmented paints (containing solids) maybe not as much. Just look at any show car, its always the clear you are looking at. I think clears are also less permeable so should act as a better seal for release agents. Having said that, Ive always used 2k catalysed car paints & they buff out real nice. Of course, wax mold release enhances this some more but take the paint finish as far as you possibly can, it helps with every step thereafter.

/pt